The purpose of this model is to understand how genetic architectures of alternative reproductive tactics impact their maintenance in populations. I’m using an individual-based simulation model with different selection scenarios, types of alternative tactics, and genetic architectures (genome-wide additive genetic variance, supergenes, expression networks) To test the model and make sure that everything has been implemented correctly, I’m first testing to ensure that the model produces the expected results without the genetic architectures.

Overview of the model

Males can be courters or not-courters and parents or not-parents. When the model is run with both traits, this results in four possible morphs: courter/parent, courter/not-parent, not-courter/parent, and not-courter/not-parent. Generations are non-overlapping and there is one reproductive bout per generation. In each generation, the population follows the following timeline:

  1. Females choose a nest
  2. Males fertilize eggs
  3. Nests survive or die
  4. Viability selection on progeny
  5. Stochastic survival to adulthood

1. Choosing a nest

A female samples 50 males and chooses a male to nest with based on his courtship trait. If there are no courtship traits in the model, she chooses based on the male’s parental trait. If she does not encouter an acceptable male, she does not nest. If she encounters multiple equally-acceptable males, she randomly selects one of them.

2. Fertilization

Once a female decides to nest, up to three males can fertilize the nest. Courters and parental males can contribute more sperm than non-courter and non-parental males: \(r_{courter}=r_{parent}=8\) and \(r_{non-courter}=r_{non-parent}=4\). A courter/non-parent has \(r_{non-parent}\) and a non-courter/parent has \(r_{parent}\). The male with whom the female is nesting gets \(r_{parent}/\Sigma{n_{sperm}}\) and additional non-parental males (up to 2) get \((r_{non-parent}*0.5/\Sigma{n_{sperm}})\), where \(\Sigma{n_{sperm}}\) is the total number of sperm contributed by all of the males, weighted by the sperm competition factor (0.5 is the default for all males except the nesting male). So, when a female mates with one courter and two non-parentals, \(\Sigma{n_{sperm}}\) = \(r_{courter}\) + 2\(*\)(0.5\(*\)\(r_{sneaker}\)), where \(r_{courter}\) = 8 and \(r_{sneaker}\) = 4, therefore \(\Sigma{n_{sperm}}\) = 12.

That being said, every time a male mates he uses his sperm, so after one mating where a courter fertilizes 50% of the female’s 4 eggs, he only has 6 sperm for his next mating.

3. Nest Survival

Before the babies can survive, the nest has to survive. This step is only relevant when parental traits are in the model - if only the courtship trait is specified, then all progeny in the nest survive at this point. When males have the parental trait, if the female has given eggs to a non-parental male (because she chose based on courtship traits), then the nest has a 10% chance of surviving. If the female has given eggs to a parental male, the nest has a 90% chance of surviving.

4. Viability selection and 5. Stochastic survival

Then the offspring experience viability selection. Courters and parental males are disfavored in viability selection, with a survival probability of 0.9950125. If an individual is both a courter and a parental male, the survival probability is 0.9900498. Non-courters and non-parental males have survival probabilities of 1. Once viability selection has been imposed, individuals die or survive randomly, and the next generation gets a chance to mate.

Evaluating equilibrium

After 10000 generations, I begin tracking the change in frequency of the courter and parent traits, and do so for 2000 additional generations. I calculate the variance in the change in frequency over those 2000 generations. I declare an equilibrium (‘stasis’) has been reached if the last change in frequency of both traits is less than the variance in changes in frequency.

Unlinked additive genetic variance

In these cases, the traits are encoded by a number (50) of loci, whose alleles contribute additively to determine the trait value. These alleles are all freely recombining and are not adhered to any physical genomic location (aka this is a classical quantitative genetics approach). The overall trait value is compared to a population-level threshold (which is static, in these cases), and if the trait value is above the threshold the male takes the parent or courter morph and if it is below he does not. Below, I’m showing the results from 10 replicates of each scenario.

Courter trait

Females choose nests based on whether the male is a courter or not, and they all prefer courters all of the time (the female preference does not have a genetic basis and does not evolve). The only way that non-courters produce offspring is through sneaking, but all males can be sneakers (both courters and non-courters). Because parental care is not incorporated in this model, all nests survive.

Frequency of the courter morph (each color represents a different replicate)

Frequency of the courter morph (each color represents a different replicate)

Of the 20 replicates, all of them reached an equilibrium by 10000 generations.

Frequency of courters in final generation
Generation CourterFreq CourterW NonCourterW
courter_unlinked_1_summary.txt_1 11999 1 1.94510 0
courter_unlinked_1_summary.txt_2 11999 1 1.97410 0
courter_unlinked_1_summary.txt_3 11999 1 1.99799 0
courter_unlinked_1_summary.txt_4 11999 1 1.98008 0
courter_unlinked_2_summary.txt_1 11999 1 1.94510 0
courter_unlinked_2_summary.txt_2 11999 1 1.97410 0
courter_unlinked_2_summary.txt_3 11999 1 1.99799 0
courter_unlinked_2_summary.txt_4 11999 1 1.98008 0
courter_unlinked_3_summary.txt_1 11999 1 1.94510 0
courter_unlinked_3_summary.txt_2 11999 1 1.97410 0
courter_unlinked_3_summary.txt_3 11999 1 1.99799 0
courter_unlinked_3_summary.txt_4 11999 1 1.98008 0
courter_unlinked_4_summary.txt_1 11999 1 1.94510 0
courter_unlinked_4_summary.txt_2 11999 1 1.97410 0
courter_unlinked_4_summary.txt_3 11999 1 1.99799 0
courter_unlinked_4_summary.txt_4 11999 1 1.98008 0
courter_unlinked_5_summary.txt_1 11999 1 1.94510 0
courter_unlinked_5_summary.txt_2 11999 1 1.97410 0
courter_unlinked_5_summary.txt_3 11999 1 1.99799 0
courter_unlinked_5_summary.txt_4 11999 1 1.98008 0

Parental trait

All females nest with parental males, so the only way non-parental males reproduce is through sneaking. Parental males provide care that allows nests to have a 90% chance of survival. The female preference does not have a genetic basis and does not evolve.

Frequency of parent morph (each color represents a different replicate)

Frequency of parent morph (each color represents a different replicate)

Frequency of parents in final generation
Generation ParentFreq ParentW NonParentW
parent_unlinked_1_summary.txt_1 11999 0.595238 1.37667 0.318627
parent_unlinked_1_summary.txt_2 11999 0.499022 1.43922 0.300781
parent_unlinked_1_summary.txt_3 11999 0.568306 1.33013 0.236287
parent_unlinked_1_summary.txt_4 11999 0.594961 1.44300 0.473684
parent_unlinked_2_summary.txt_1 11999 0.595238 1.37667 0.318627
parent_unlinked_2_summary.txt_2 11999 0.499022 1.43922 0.300781
parent_unlinked_2_summary.txt_3 11999 0.568306 1.33013 0.236287
parent_unlinked_2_summary.txt_4 11999 0.594961 1.44300 0.473684
parent_unlinked_3_summary.txt_1 11999 0.569260 1.41667 0.202643
parent_unlinked_3_summary.txt_2 11999 0.596838 1.41391 0.382353
parent_unlinked_3_summary.txt_3 11999 0.569288 1.31908 0.347826
parent_unlinked_3_summary.txt_4 11999 0.536062 1.28364 0.231092
parent_unlinked_4_summary.txt_1 11999 0.595238 1.37667 0.318627
parent_unlinked_4_summary.txt_2 11999 0.499022 1.43922 0.300781
parent_unlinked_4_summary.txt_3 11999 0.568306 1.33013 0.236287
parent_unlinked_4_summary.txt_4 11999 0.594961 1.44300 0.473684
parent_unlinked_5_summary.txt_1 11999 0.595238 1.37667 0.318627
parent_unlinked_5_summary.txt_2 11999 0.499022 1.43922 0.300781
parent_unlinked_5_summary.txt_3 11999 0.568306 1.33013 0.236287
parent_unlinked_5_summary.txt_4 11999 0.594961 1.44300 0.473684

Variation was maintained in 20 of the 20. 0 of the 20 populations crashed, though. Of the 20 replicates, 20 reached an equilibrium by 10000 generations.

Courtship and Parental Traits

Females choose nests based on males’ courtship trait (they all only nest with courting males, and the female preference does not have a genetic basis and does not evolve), and then the survival of the nest depends on whether the courting male is also a parental male. If the chosen male is a parental male, the nest has a 90% chance of survival. Otherwise, it only has a 10% chance. Non-courters only reproduce through sneaking.

The different runs have different outcomes.

Let’s look at the morph frequencies.

Frequency of the 4 morphs in each rep

Frequency of the 4 morphs in each rep

In some of the runs the population crashed after few generations. This is obvious when looking at the the final frequencies in a table as well:

Frequency of morphs in final generation
Generation CourterFreq CourterW NonCourterW FreqNcNp
parent-courter_unlinked_1_summary.txt_1 11999 0.574181 0.335570 0 0
parent-courter_unlinked_1_summary.txt_2 11999 0.576108 0.327759 0 0
parent-courter_unlinked_1_summary.txt_3 11999 0.575342 0.278912 0 0
parent-courter_unlinked_1_summary.txt_4 11999 0.569745 0.337931 0 0
parent-courter_unlinked_2_summary.txt_1 11999 0.574181 0.335570 0 0
parent-courter_unlinked_2_summary.txt_2 11999 0.576108 0.327759 0 0
parent-courter_unlinked_2_summary.txt_3 11999 0.575342 0.278912 0 0
parent-courter_unlinked_2_summary.txt_4 11999 0.569745 0.337931 0 0
parent-courter_unlinked_3_summary.txt_1 11999 0.574757 0.291525 0 0
parent-courter_unlinked_3_summary.txt_2 11999 0.586667 0.344156 0 0
parent-courter_unlinked_3_summary.txt_3 11999 0.576923 0.383333 0 0
parent-courter_unlinked_3_summary.txt_4 11999 0.586466 0.326923 0 0
parent-courter_unlinked_4_summary.txt_1 11999 0.574181 0.335570 0 0
parent-courter_unlinked_4_summary.txt_2 11999 0.576108 0.327759 0 0
parent-courter_unlinked_4_summary.txt_3 11999 0.575342 0.278912 0 0
parent-courter_unlinked_4_summary.txt_4 11999 0.569745 0.337931 0 0
parent-courter_unlinked_5_summary.txt_1 11999 0.574757 0.291525 0 0
parent-courter_unlinked_5_summary.txt_2 11999 0.586667 0.344156 0 0
parent-courter_unlinked_5_summary.txt_3 11999 0.576923 0.383333 0 0
parent-courter_unlinked_5_summary.txt_4 11999 0.586466 0.326923 0 0

Multiple morphs are maintained in 20 of the 20 replicates, and those morphs contain either a parent or a courter. However, 0 of those reps with variation actually crashed.

Linked additive genetic variance

Courter trait

Frequency of the courter morph with linked QTLs (each color represents a different replicate)

Frequency of the courter morph with linked QTLs (each color represents a different replicate)

Of the 20 replicates, 0 reached an equilibrium by 10000 generations.

Frequency of courters with linked QTLs in final generation
CourterFreq CourterW NonCourterW
courter_linked_1_summary.txt_1 1 2.02439 0
courter_linked_1_summary.txt_2 1 2.01616 0
courter_linked_1_summary.txt_3 1 1.95866 0
courter_linked_1_summary.txt_4 1 1.93786 0
courter_linked_2_summary.txt_1 1 2.02439 0
courter_linked_2_summary.txt_2 1 2.01616 0
courter_linked_2_summary.txt_3 1 1.95866 0
courter_linked_2_summary.txt_4 1 1.93786 0
courter_linked_3_summary.txt_1 1 2.05372 0
courter_linked_3_summary.txt_2 1 2.10805 0
courter_linked_3_summary.txt_3 1 1.99000 0
courter_linked_3_summary.txt_4 1 2.01826 0
courter_linked_4_summary.txt_1 1 1.92486 0
courter_linked_4_summary.txt_2 1 2.04733 0
courter_linked_4_summary.txt_3 1 2.04321 0
courter_linked_4_summary.txt_4 1 2.03265 0
courter_linked_5_summary.txt_1 1 2.00811 0
courter_linked_5_summary.txt_2 1 1.90249 0
courter_linked_5_summary.txt_3 1 2.08386 0
courter_linked_5_summary.txt_4 1 1.91171 0

Every rep has the courtship trait go to fixation.

Parental trait

All females nest with parental males, so the only way non-parental males reproduce is through sneaking. Parental males provide care that allows nests to have a 90% chance of survival. The female preference does not have a genetic basis and does not evolve.

Frequency of parent morph with linked QTLs (each color represents a different replicate)

Frequency of parent morph with linked QTLs (each color represents a different replicate)

Frequency of parents with linked QTLs in final generation
ParentFreq ParentW NonParentW
parent_linked_1_summary.txt_1 0.751491 1.65344 0.368000
parent_linked_1_summary.txt_2 0.857143 1.64352 0.597222
parent_linked_1_summary.txt_3 0.817658 1.62207 0.505263
parent_linked_1_summary.txt_4 0.845679 1.63504 0.480000
parent_linked_2_summary.txt_1 0.751491 1.65344 0.368000
parent_linked_2_summary.txt_2 0.857143 1.64352 0.597222
parent_linked_2_summary.txt_3 0.817658 1.62207 0.505263
parent_linked_2_summary.txt_4 0.845679 1.63504 0.480000
parent_linked_3_summary.txt_1 0.887379 1.61488 0.793103
parent_linked_3_summary.txt_2 0.868821 1.60613 0.507246
parent_linked_3_summary.txt_3 0.886905 1.61745 0.807018
parent_linked_3_summary.txt_4 0.885892 1.67213 0.909090
parent_linked_4_summary.txt_1 0.850932 1.67640 0.583333
parent_linked_4_summary.txt_2 0.879276 1.00000 NA
parent_linked_4_summary.txt_3 0.862745 1.64091 0.528571
parent_linked_4_summary.txt_4 0.867220 1.77751 0.859375
parent_linked_5_summary.txt_1 0.882812 1.66593 0.566667
parent_linked_5_summary.txt_2 0.886640 1.57534 0.928571
parent_linked_5_summary.txt_3 0.871849 1.74458 0.639344
parent_linked_5_summary.txt_4 0.880000 1.68182 0.912281

Variation was maintained in 20 of the 20. 20 of the 20 populations crashed, though. Of the 20 replicates, 0 reached an equilibrium by 10000 generations.

Courtship and Parental Traits

Females choose nests based on males’ courtship trait (they all only nest with courting males, and the female preference does not have a genetic basis and does not evolve), and then the survival of the nest depends on whether the courting male is also a parental male. If the chosen male is a parental male, the nest has a 90% chance of survival. Otherwise, it only has a 10% chance. Non-courters only reproduce through sneaking.

Frequency of the two morphs with linked QTLs (courter = green, parent = blue)

Frequency of the two morphs with linked QTLs (courter = green, parent = blue)

The different runs have different outcomes.

Let’s look at the morph frequencies.

Frequency of the 4 morphs in each rep with linked QTLs

Frequency of the 4 morphs in each rep with linked QTLs

Frequency of the 4 morphs in each rep with linked QTLs

Frequency of the 4 morphs in each rep with linked QTLs

In some of the runs the population crashed after few generations. This is obvious when looking at the the final frequencies in a table as well:

Frequency of morphs in final generation (linked loci)
Generation CourterFreq CourterW NonCourterW FreqNcNp
parent-courter_linked_1_summary.txt_1 2858 0.888438 1.933790 0.8909090 0.0933063
parent-courter_linked_1_summary.txt_2 2858 0.902344 1.642860 0.0000000 NA
parent-courter_linked_1_summary.txt_3 2057 0.900362 1.700200 0.8545450 0.0923913
parent-courter_linked_1_summary.txt_4 2857 0.886905 1.807610 0.9473680 0.0932540
parent-courter_linked_1_summary.txt_5 2857 0.902724 1.745690 0.9800000 0.0836576
parent-courter_linked_2_summary.txt_1 0 0.487854 0.240664 0.0000000 0.0000000
parent-courter_linked_2_summary.txt_2 3695 0.576497 0.457692 0.0000000 0.0000000
parent-courter_linked_2_summary.txt_3 117 0.529817 0.411255 0.0000000 0.0000000
parent-courter_linked_2_summary.txt_4 111 0.523702 0.284483 0.0000000 0.0000000
parent-courter_linked_2_summary.txt_5 110 0.520971 0.322034 0.0000000 0.0000000
parent-courter_linked_2_summary.txt_6 1 0.506329 0.383333 0.0000000 0.0000000
parent-courter_linked_2_summary.txt_7 0 0.487854 0.385892 0.0000000 0.0000000
parent-courter_linked_2_summary.txt_8 3695 0.568849 0.341270 0.0000000 0.0000000
parent-courter_linked_2_summary.txt_9 513 0.535632 0.369099 0.0000000 0.0000000
parent-courter_linked_2_summary.txt_10 192 0.535469 0.504274 0.0000000 0.0000000
parent-courter_linked_2_summary.txt_11 1 0.505353 0.351695 0.0000000 0.0000000
parent-courter_linked_2_summary.txt_12 0 0.487854 0.311203 0.0000000 0.0000000
parent-courter_linked_2_summary.txt_13 3695 0.566810 0.433460 0.0000000 0.0000000
parent-courter_linked_2_summary.txt_14 1 0.505263 0.458333 0.0000000 0.0000000
parent-courter_linked_2_summary.txt_15 0 0.487854 0.506224 0.0000000 0.0000000
parent-courter_linked_2_summary.txt_16 3695 0.570513 0.000000 NA NA
parent-courter_linked_3_summary.txt_1 0 0.487854 0.240664 0.0000000 0.0000000
parent-courter_linked_3_summary.txt_2 3642 0.556818 0.450820 0.0000000 0.0000000
parent-courter_linked_3_summary.txt_3 117 0.529817 0.411255 0.0000000 0.0000000
parent-courter_linked_3_summary.txt_4 111 0.523702 0.284483 0.0000000 0.0000000
parent-courter_linked_3_summary.txt_5 110 0.520971 0.322034 0.0000000 0.0000000
parent-courter_linked_3_summary.txt_6 1 0.506329 0.383333 0.0000000 0.0000000
parent-courter_linked_3_summary.txt_7 0 0.487854 0.385892 0.0000000 0.0000000
parent-courter_linked_3_summary.txt_8 3642 0.576837 0.262548 0.0000000 0.0000000
parent-courter_linked_3_summary.txt_9 513 0.535632 0.369099 0.0000000 0.0000000
parent-courter_linked_3_summary.txt_10 192 0.535469 0.504274 0.0000000 0.0000000
parent-courter_linked_3_summary.txt_11 1 0.505353 0.351695 0.0000000 0.0000000
parent-courter_linked_3_summary.txt_12 0 0.487854 0.311203 0.0000000 0.0000000
parent-courter_linked_3_summary.txt_13 3641 0.569296 0.355805 0.0000000 0.0000000
parent-courter_linked_3_summary.txt_14 1 0.505263 0.458333 0.0000000 0.0000000
parent-courter_linked_3_summary.txt_15 0 0.487854 0.506224 0.0000000 0.0000000
parent-courter_linked_3_summary.txt_16 3641 0.564378 0.353612 0.0000000 0.0000000
parent-courter_linked_4_summary.txt_1 0 0.487854 0.381743 0.0000000 0.0000000
parent-courter_linked_4_summary.txt_2 3700 0.557269 0.272727 0.0000000 0.0000000
parent-courter_linked_4_summary.txt_3 1 0.504310 0.367521 0.0043478 0.0021552
parent-courter_linked_4_summary.txt_4 0 0.487854 0.502075 0.0000000 0.0000000
parent-courter_linked_4_summary.txt_5 3700 0.567164 0.383459 0.0000000 0.0000000
parent-courter_linked_4_summary.txt_6 0 0.487854 0.481328 0.0000000 0.0000000
parent-courter_linked_4_summary.txt_7 3700 NA NA NA NA
parent-courter_linked_4_summary.txt_8 0 0.487854 0.452282 0.0000000 0.0000000
parent-courter_linked_4_summary.txt_9 3699 0.565957 0.379699 0.0000000 0.0000000
parent-courter_linked_5_summary.txt_1 0 0.487854 0.381743 0.0000000 0.0000000
parent-courter_linked_5_summary.txt_2 3524 0.567982 0.428571 0.0000000 0.0000000
parent-courter_linked_5_summary.txt_3 1 0.504310 0.367521 0.0043478 0.0021552
parent-courter_linked_5_summary.txt_4 0 0.487854 0.502075 0.0000000 0.0000000
parent-courter_linked_5_summary.txt_5 3524 0.570526 0.372694 0.0000000 0.0021053
parent-courter_linked_5_summary.txt_6 0 0.487854 0.481328 0.0000000 0.0000000
parent-courter_linked_5_summary.txt_7 3523 0.554839 0.344961 0.0000000 0.0000000
parent-courter_linked_5_summary.txt_8 0 0.487854 0.452282 0.0000000 0.0000000
parent-courter_linked_5_summary.txt_9 3523 0.565032 0.305660 0.0000000 0.0000000

Multiple morphs are maintained in 37 of the 55 replicates, and those morphs contain either a parent or a courter. However, 55 of those reps with variation actually crashed.

Supergenes

Courter trait

Frequency of the courter morph with supergenes (each color represents a different replicate)

Frequency of the courter morph with supergenes (each color represents a different replicate)

Of the 20 replicates, 0 reached an equilibrium by 10000 generations.

Frequency of courters with supergenes in final generation
CourterFreq CourterW NonCourterW
courter_supergene_1_summary.txt_1 1 2.06004 0
courter_supergene_1_summary.txt_2 1 2.02028 0
courter_supergene_1_summary.txt_3 1 2.02236 0
courter_supergene_1_summary.txt_4 1 1.91715 0
courter_supergene_2_summary.txt_1 1 1.95678 0
courter_supergene_2_summary.txt_2 1 1.93010 0
courter_supergene_2_summary.txt_3 1 1.92248 0
courter_supergene_2_summary.txt_4 1 2.14255 0
courter_supergene_3_summary.txt_1 1 2.14378 0
courter_supergene_3_summary.txt_2 1 1.89354 0
courter_supergene_3_summary.txt_3 1 1.94347 0
courter_supergene_3_summary.txt_4 1 2.03067 0
courter_supergene_4_summary.txt_1 1 2.01008 0
courter_supergene_4_summary.txt_2 1 2.02648 0
courter_supergene_4_summary.txt_3 1 1.91154 0
courter_supergene_4_summary.txt_4 1 2.14409 0
courter_supergene_5_summary.txt_1 1 2.04938 0
courter_supergene_5_summary.txt_2 1 2.05372 0
courter_supergene_5_summary.txt_3 1 2.15435 0
courter_supergene_5_summary.txt_4 1 1.90421 0

Parental trait

All females nest with parental males, so the only way non-parental males reproduce is through sneaking. Parental males provide care that allows nests to have a 90% chance of survival. The female preference does not have a genetic basis and does not evolve.

Frequency of parent morph with supergenes (each color represents a different replicate)

Frequency of parent morph with supergenes (each color represents a different replicate)

Frequency of parents with supergenes in final generation
ParentFreq ParentW NonParentW
parent_supergene_1_summary.txt_1 0.529524 1.35612 0.194332
parent_supergene_1_summary.txt_2 0.497041 1.38492 0.321569
parent_supergene_1_summary.txt_3 0.594286 1.44872 0.211268
parent_supergene_1_summary.txt_4 0.556190 1.46575 0.231760
parent_supergene_2_summary.txt_1 0.796117 1.53171 0.580952
parent_supergene_2_summary.txt_2 0.806773 1.51605 0.525773
parent_supergene_2_summary.txt_3 0.778008 1.66933 0.439252
parent_supergene_2_summary.txt_4 0.830303 1.67883 0.726190
parent_supergene_3_summary.txt_1 0.809917 1.64796 0.630435
parent_supergene_3_summary.txt_2 0.766208 1.54615 0.529412
parent_supergene_3_summary.txt_3 0.799595 1.55443 0.636364
parent_supergene_3_summary.txt_4 0.828402 1.58571 0.517241
parent_supergene_4_summary.txt_1 0.809917 1.64796 0.630435
parent_supergene_4_summary.txt_2 0.766208 1.54615 0.529412
parent_supergene_4_summary.txt_3 0.799595 1.55443 0.636364
parent_supergene_4_summary.txt_4 0.828402 1.58571 0.517241
parent_supergene_5_summary.txt_1 0.809917 1.64796 0.630435
parent_supergene_5_summary.txt_2 0.766208 1.54615 0.529412
parent_supergene_5_summary.txt_3 0.799595 1.55443 0.636364
parent_supergene_5_summary.txt_4 0.828402 1.58571 0.517241

Variation was maintained in 20 of the 20. 20 of the 20 populations crashed, though. Of the 20 replicates, 0 reached an equilibrium by 10000 generations.

Courtship and Parental Traits

Females choose nests based on males’ courtship trait (they all only nest with courting males, and the female preference does not have a genetic basis and does not evolve), and then the survival of the nest depends on whether the courting male is also a parental male. If the chosen male is a parental male, the nest has a 90% chance of survival. Otherwise, it only has a 10% chance. Non-courters only reproduce through sneaking.

Frequency of the two morphs with linked QTLs (courter = green, parent = blue)

Frequency of the two morphs with linked QTLs (courter = green, parent = blue)

The different runs have different outcomes.

Let’s look at the morph frequencies.

Frequency of the 4 morphs in each rep with supergenes

Frequency of the 4 morphs in each rep with supergenes

Frequency of the 4 morphs in each rep with supergenes

Frequency of the 4 morphs in each rep with supergenes

In some of the runs the population crashed after few generations. This is obvious when looking at the the final frequencies in a table as well:

Frequency of morphs in final generation (supergenes)
Generation CourterFreq CourterW NonCourterW FreqNcNp
parent-courter_supergene_1_summary.txt_1 0 0.487854 0.423237 0 0
parent-courter_supergene_1_summary.txt_2 3491 0.559633 0.454918 0 0
parent-courter_supergene_1_summary.txt_3 3243 0.537037 0.400862 0 0
parent-courter_supergene_1_summary.txt_4 3242 0.539683 0.231092 0 0
parent-courter_supergene_1_summary.txt_5 239 0.535714 0.391667 0 0
parent-courter_supergene_1_summary.txt_6 0 0.487854 0.460581 0 0
parent-courter_supergene_1_summary.txt_7 3491 NA NA NA NA
parent-courter_supergene_1_summary.txt_8 0 0.487854 0.431535 0 0
parent-courter_supergene_1_summary.txt_9 3490 0.563715 0.386973 0 0
parent-courter_supergene_1_summary.txt_10 0 0.487854 0.414938 0 0
parent-courter_supergene_1_summary.txt_11 3490 0.578834 0.410448 0 0
parent-courter_supergene_2_summary.txt_1 0 0.487854 0.423237 0 0
parent-courter_supergene_2_summary.txt_2 3482 0.569820 0.464286 0 NA
parent-courter_supergene_2_summary.txt_3 3243 0.537037 0.400862 0 0
parent-courter_supergene_2_summary.txt_4 3242 0.539683 0.231092 0 0
parent-courter_supergene_2_summary.txt_5 239 0.535714 0.391667 0 0
parent-courter_supergene_2_summary.txt_6 0 0.487854 0.460581 0 0
parent-courter_supergene_2_summary.txt_7 3481 0.573876 0.384328 0 0
parent-courter_supergene_2_summary.txt_8 0 0.487854 0.431535 0 0
parent-courter_supergene_2_summary.txt_9 3481 0.556745 0.334615 0 0
parent-courter_supergene_2_summary.txt_10 0 0.487854 0.414938 0 0
parent-courter_supergene_2_summary.txt_11 3481 0.568966 0.397727 0 0
parent-courter_supergene_3_summary.txt_1 0 0.487854 0.423237 0 0
parent-courter_supergene_3_summary.txt_2 3655 0.579646 0.297710 0 0
parent-courter_supergene_3_summary.txt_3 3243 0.537037 0.400862 0 0
parent-courter_supergene_3_summary.txt_4 3242 0.539683 0.231092 0 0
parent-courter_supergene_3_summary.txt_5 239 0.535714 0.391667 0 0
parent-courter_supergene_3_summary.txt_6 0 0.487854 0.460581 0 0
parent-courter_supergene_3_summary.txt_7 3655 0.569002 0.343284 0 0
parent-courter_supergene_3_summary.txt_8 0 0.487854 0.431535 0 0
parent-courter_supergene_3_summary.txt_9 3655 0.570213 0.406716 0 0
parent-courter_supergene_3_summary.txt_10 0 0.487854 0.414938 0 0
parent-courter_supergene_3_summary.txt_11 3654 0.571429 0.386364 0 0
parent-courter_supergene_4_summary.txt_1 0 0.487854 0.423237 0 0
parent-courter_supergene_4_summary.txt_2 3673 0.576837 0.366795 0 0
parent-courter_supergene_4_summary.txt_3 3243 0.537037 0.400862 0 0
parent-courter_supergene_4_summary.txt_4 3242 0.539683 0.231092 0 0
parent-courter_supergene_4_summary.txt_5 239 0.535714 0.391667 0 0
parent-courter_supergene_4_summary.txt_6 0 0.487854 0.460581 0 0
parent-courter_supergene_4_summary.txt_7 3673 0.570815 0.289474 0 0
parent-courter_supergene_4_summary.txt_8 0 0.487854 0.431535 0 0
parent-courter_supergene_4_summary.txt_9 3673 0.571429 0.320896 0 0
parent-courter_supergene_4_summary.txt_10 0 0.487854 0.414938 0 0
parent-courter_supergene_4_summary.txt_11 3673 0.573276 0.379699 0 0
parent-courter_supergene_5_summary.txt_1 0 0.487854 0.423237 0 0
parent-courter_supergene_5_summary.txt_2 3692 0.576837 0.459459 0 0
parent-courter_supergene_5_summary.txt_3 3243 0.537037 0.400862 0 0
parent-courter_supergene_5_summary.txt_4 3242 0.539683 0.231092 0 0
parent-courter_supergene_5_summary.txt_5 239 0.535714 0.391667 0 0
parent-courter_supergene_5_summary.txt_6 0 0.487854 0.460581 0 0
parent-courter_supergene_5_summary.txt_7 3691 0.566596 0.425373 0 0
parent-courter_supergene_5_summary.txt_8 0 0.487854 0.431535 0 0
parent-courter_supergene_5_summary.txt_9 3691 0.563043 0.440154 0 0
parent-courter_supergene_5_summary.txt_10 0 0.487854 0.414938 0 0
parent-courter_supergene_5_summary.txt_11 3691 0.571116 0.379310 0 0

Multiple morphs are maintained in 34 of the 55 replicates, and those morphs contain either a parent or a courter. However, 55 of those reps with variation actually crashed.